Structure of a peptide-based photo-affinity cross-linker with herceptin Fc

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 50% strand (DSSP).

Ligands and binding sites

• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
• MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
• BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
• FUL · beta-L-fucopyranose · sugar · chains A
• FUC · alpha-L-fucopyranose · sugar · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 1142 Ų buried · 4 hydrogen bonds · protein-protein
• A–E · 692 Ų buried · 9 hydrogen bonds · protein-protein
• B–F · 678 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 2 glycan, 2 modified (disulfide, N-glycosylation, nonstandard).

Compared structures

• 6N9T · Structure of a peptide-based photo-affinity cross-linker with Herceptin Fc · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q6MZV7
• Elsewhere: RCSB PDB 6N9T · PDBe 6N9T · UniProt Q6MZV7